Project Summary: Though a reference human genome and even excellent characterization of the epigenome (ENCODE, Epigenetics Roadmap) has been generated, the significance of noncoding genetic or epigenetic changes is still far from clear. With the advent of affordable DNA- sequencing technologies, methods have been developed for examining nuclear organization, chromatin state/histone post translation modifications, chromatin accessibility and methylation state. But these methods do not directly interrogate the DNA strand, and the reads are typically too short to provide critical correlative information. We propose the development of a novel epigenetic characterization methodology, fundamentally through the practical implementation of the sequencing of modified bases using a nanopore sequencing platform. Nanopore sequencing directly probes the chemical structure of the molecule in the pore with exquisite sensitivity. Its long reads enable correlation of epigenetic state over large (>10kb) stretches of the genome; each of these reads originates from a single cell, probing the epigenetic heterogeneity of the sample.